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rrwick / Porechop

adapter trimmer for Oxford Nanopore reads
GNU General Public License v3.0
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Installation in Singularity xenial image #55

Open mbhall88 opened 6 years ago

mbhall88 commented 6 years ago

Hi Ryan,

This isn't an issue really, more just noting this somewhere incase someone else comes across it. I was having some difficulty with getting porechop to work in a singularity container and thought I would share a couple of simple things I had to do to get it working

PORECHOP_VERSION=0.2.3
apt-get install -y python3-setuptools python3-pkg-resources
wget https://github.com/rrwick/Porechop/archive/v${PORECHOP_VERSION}.tar.gz
tar xzf v${PORECHOP_VERSION}.tar.gz
rm v${PORECHOP_VERSION}.tar.gz
cd Porechop-${PORECHOP_VERSION}
python3 setup.py install

This is the code I had to run in my Singularity recipe to get porechop working, otherwise it was throwing an error complaining about ImportError: No module named 'pkg_resources'. I know you noted something about this in the README.
The key was the apt-get install -y python3-setuptools python3-pkg-resources. I had previously been trying to pip3 install setuptools but wasn't having any luck.

Hope this helps someone.

btemperton commented 5 years ago

Glad you put this up, just hit this error and solved it using this post. Thanks!